What is quantitative enrichment analysis (QEA)?

MetaboAnalyst offers three types of enrichment analysis for targeted metabolomics, including

  • Over Representation Analysis (ORA, input: significant compound names)
  • Single Sample Profiling (SSP, input: a complete sample profile)
  • Quantitative Enrichment Analysis (QEA, input: a complete concentration table)

QEA is based on compound concentration table. It is often claimed to be more sensitive than ORA and has the potential to discover “subtle but consistent” changes among compounds within the same biological pathway.

Many algorithms have been developed in the last decade for this type of enrichment analysis, the most famous being the Gene Set Enrichment Analysis. Many new and improved methods have since been implemented. When users upload concentration tables, GlobalTest is used for functional enrichment analysis; for pathway enrichment analysis, users can choose between GlobalTest or GlobalAncova.

Some important features about these two methods include that they support binary, multi-group, as well as continuous phenotypes, and p values can be approximated efficiently based on the asymptotic distribution without using permutations, which is critical for developing web applications.

Hello. I’ve been trying to do this analysis on a continuous phenotype but I cannot upload the csv file. I had set the layout to the same as the sample dataset and I just keep receiving ‘unknown error occurred’.

The issue should be fixed now. Thanks for the note

Hi! What are the statistical tests actually performed in the QEA? I can’t understand it from the documentation. Thanks in advance

The algorithm is based on globaltest - you can find more statistical details from the reference in the top post.


I am using QEA and cannot get the names/ID to match. I have used your Compound ID conversion but it seems the databases do not match. I have tried with HMDB ID’s first because my understanding is that those will register more hits in QEA. However, both HMDB and the Common Compound names are not fully registering between the two. Only half of my metabolites pop up in the Name Check tab. Originally, I used Pubmed CID’s from my own data but that also failed. How can I fix this?


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